5-547743-A-G

Variant names:

• chr5-547743-A-G
• rs4957070

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.489 in 152,148 control chromosomes in the GnomAD database, including 21,601 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (21601 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74267 AN: 152028 Hom.: 21557 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.461

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.489 AC: 74360 AN: 152148 Hom.: 21601 Cov.: 33 AF XY: 0.481 AC XY: 35784 AN XY: 74376

African (AFR) AF: 0.821 AC: 34072 AN: 41512

American (AMR) AF: 0.470 AC: 7191 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1239 AN: 5158

South Asian (SAS) AF: 0.487 AC: 2352 AN: 4830

European-Finnish (FIN) AF: 0.216 AC: 2286 AN: 10604

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24337 AN: 67968

Other (OTH) AF: 0.461 AC: 974 AN: 2114

Alfa AF: 0.549 Hom.: 9523

Bravo AF: 0.519

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4957070; hg19: chr5-547858; COSMIC: COSV60122519;